Fast atom bombardment (FAB) has become one of the most widely utilized techniques for obtaining mass spectra of thermally labile and/or very polar substances. In conjunction with tandem MS (MS-MS), the fragmentation information so vital for structure elucidation can be obtained from ions normally not observed to fragment and from mixtures where the parent ion-daughter ion relationships are not known. This project involves three areas: 1) instrumental developments in MS-MS; 2) determination of underlying structural features which influence the spectra obtained so that data from unknowns can more easily be used for structure elucidation; and 3) application of FAB/MS and FAB/MS-MS for structure elucidation. As part of the instrumental development we have extended our present instrument capabilities from MS-MS to MS-MS-MS-MS (MS4). With MS4, the consecutive fragmentations of a molecule can be followed. In the determination of structural effects on MS-MS data, we have investigated the effects various N- and C-terminal amino acids have on the data and the utility of MS-MS spectra of (M+Na)+ ions of peptides for sequencing peptides. We have applied FAB/MS and FAB/MS-MS to the structure elucidation of chemically modified analogs of Leu-enkephalin in which a CH2S moiety replaces as amide linkage, to the structure elucidation of phospholipids containing unusual fatty acids and head groups, to the differentiation of steroid glucuronide stereoisomers by MS-MS, and to the characterization of cross- linked peptides.